Different types of tools are used to perform hundreds of processing operations during processing of wafers (i.e. semiconductor substrates) in wafer processing systems. Most of these operations are performed in vacuum chambers (i.e., process chambers) of a wafer processing system at very low pressure. Other operations are performed at atmospheric pressure in controlled environments of filtered air or an inert gas. Wafers are introduced to the process chambers with wafer handling systems that are mechanically coupled to respective process chambers. The wafer handling systems transfer wafers from the factory floor to the process chamber. Wafer handling systems can include, for example, equipment front end modules (EFEMs) which are operable to transfer wafers from a front opening unified pod (FOUP) to the wafer processing system for processing and back to the FOUP, load locks to bring the wafers from atmospheric conditions to very low pressure conditions (e.g., vacuum conditions) and back to atmospheric conditions wherein robots transfer the wafers to various positions in the wafer processing system. Throughput (i.e., the number of wafers that are processed in a period of time) is affected by the wafer processing time, the number of wafers that are processed at a given time, as well as timing of the steps to introduce the wafers into the vacuum chambers. Thus, improved methods and apparatuses which increase throughput are needed.